Contacts of the strand formed by residues 129 - 135 (chain B) in PDB entry 5E1M


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with TYR 129 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  CYS*     3.6    11.7    -      -       -      +
     65B  ALA      3.7    19.5    -      -       -      -
     66B  LEU*     3.7    30.1    -      -       +      +
     88B  ASP*     2.6    36.0    +      -       -      +
    112B  ARG*     3.7    13.8    +      -       -      -
    115B  PHE*     3.9     9.9    -      -       -      -
    122B  PHE*     5.0     1.0    -      -       -      -
    124B  PRO*     3.8    22.6    -      -       +      +
    125B  GLU*     4.5     6.7    +      -       -      +
    128B  SER*     1.3    92.6    -      -       -      +
    130B  ASP*     1.3    62.1    +      -       -      +
    131B  VAL      3.9     6.3    -      -       -      +
    132B  ILE*     3.8    19.7    -      -       +      -
    156B  SER*     3.0    22.4    +      -       -      +
    157B  LEU*     3.3     9.2    -      -       -      +
    158B  ARG*     2.9    26.9    +      -       -      +
    161B  GLY*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  THR*     3.5     4.0    -      -       +      +
     61B  GLY*     3.2    42.2    +      -       -      +
     63B  SER*     2.6    40.9    +      -       -      -
     64B  CYS      2.8    14.6    +      -       -      +
     84B  PHE*     4.2     3.4    -      -       +      -
    129B  TYR*     1.3    72.4    -      -       -      +
    131B  VAL*     1.3    63.5    +      -       -      +
    157B  LEU*     4.6     0.4    -      -       -      -
    158B  ARG*     3.5    22.1    +      -       -      +
    159B  PRO      4.6     4.2    -      -       -      +
    161B  GLY*     3.0     9.2    -      -       -      -
    162B  ILE      2.9    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LEU*     4.0    21.1    -      -       +      -
     60B  THR*     3.8    14.1    -      -       +      -
     64B  CYS      3.6     2.4    +      -       -      -
     65B  ALA*     3.1     8.9    -      -       +      +
     66B  LEU      2.9    23.9    +      -       -      +
     80B  LEU*     4.9     1.1    -      -       +      -
     84B  PHE*     3.4    34.1    -      -       +      -
    129B  TYR*     3.9     1.2    -      -       -      +
    130B  ASP*     1.3    85.8    -      -       -      +
    132B  ILE*     1.3    75.0    -      -       -      +
    133B  TRP*     4.1    25.1    -      -       +      +
    162B  ILE*     3.3    14.6    -      -       +      +
    164B  VAL*     4.8     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU*     3.5    10.1    -      -       +      -
     68B  CYS*     3.7    26.2    -      -       -      -
    129B  TYR*     3.8    19.3    -      -       +      -
    131B  VAL*     1.3    78.9    -      -       -      +
    133B  TRP*     1.3    56.3    +      -       -      +
    134B  ILE*     4.0     7.9    -      -       +      -
    153B  CYS*     3.5    39.3    -      -       +      +
    156B  SER*     3.2    27.1    -      -       -      +
    157B  LEU*     3.7    14.6    -      -       +      -
    162B  ILE      3.0     6.1    +      -       -      -
    163B  ILE*     3.3    10.4    -      -       +      +
    164B  VAL      2.8    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  SER*     3.5    40.2    -      -       -      -
     48B  PHE*     4.8     5.2    -      +       -      -
     49B  LEU*     4.0    20.6    -      -       +      -
     65B  ALA*     6.1     0.2    -      -       +      -
     66B  LEU      2.8    12.8    +      -       -      +
     67B  ASP*     3.7     4.2    -      -       -      +
     68B  CYS*     2.8    33.8    +      -       -      +
     75B  ILE*     3.9    21.7    -      -       +      +
     79B  LEU*     3.7    25.1    -      -       +      -
     80B  LEU*     4.3    17.0    -      -       +      -
    131B  VAL*     4.0    13.2    -      -       +      -
    132B  ILE*     1.3    71.5    -      -       -      +
    134B  ILE*     1.3    58.3    +      -       -      +
    135B  GLN*     2.9    36.3    +      -       +      +
    164B  VAL*     3.7    45.8    -      -       +      -
    166B  LYS*     4.5     7.5    -      -       +      +
    219B  SER*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  CYS*     3.9    21.1    -      -       +      -
    119B  LEU*     4.6     6.1    -      -       +      -
    132B  ILE*     4.0     9.0    -      -       +      +
    133B  TRP*     1.3    78.0    -      -       -      +
    135B  GLN*     1.3    58.9    +      -       -      +
    136B  TRP      4.3     0.2    +      -       -      -
    137B  VAL*     3.6    22.7    -      -       +      -
    138B  ILE*     3.7    20.2    -      -       +      +
    146B  LEU*     5.8     1.1    -      -       +      -
    149B  PHE*     3.9    17.3    -      -       +      -
    150B  LEU*     3.8    19.3    -      -       +      -
    153B  CYS*     4.4     1.1    -      -       -      -
    163B  ILE*     3.7    25.6    -      -       +      -
    164B  VAL      2.8    13.3    +      -       -      +
    165B  ILE*     3.3    10.0    -      -       +      +
    166B  LYS      2.9    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  ASP*     2.8    31.3    +      -       -      +
     42B  ILE*     6.0     0.2    -      -       -      +
     45B  SER*     4.0     2.8    +      -       -      -
     67B  ASP*     5.6     0.2    +      -       -      -
     68B  CYS      3.9     6.7    +      -       -      +
     74B  ARG*     4.1     0.2    -      -       -      -
     75B  ILE*     3.4    25.3    -      -       +      +
    133B  TRP*     2.9    32.5    +      -       -      +
    134B  ILE*     1.3    75.6    -      -       -      +
    136B  TRP*     1.3    97.3    +      -       +      +
    137B  VAL*     3.2     6.4    +      -       -      +
    166B  LYS*     3.1    32.1    -      -       +      +
    301B  SAH      2.8    26.8    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il